GapMind for catabolism of small carbon sources

 

Alignments for a candidate for hcrC in Ruegeria conchae TW15

Align 4-hydroxybenzoyl-CoA reductase, γ subunit (EC 1.3.7.9) (characterized)
to candidate WP_010442647.1 G7G_RS0116990 molybdopterin-dependent oxidoreductase

Query= metacyc::MONOMER-14378
         (158 letters)



>NCBI__GCF_000192475.1:WP_010442647.1
          Length = 911

 Score =  138 bits (348), Expect = 2e-37
 Identities = 67/143 (46%), Positives = 97/143 (67%), Gaps = 1/143 (0%)

Query: 9   VNGRPREDAVAGNALLIDYLRDTLGLTGTKQGCDGGECGACTVLVDGQPRLACCTLAHSV 68
           +NGR     +     L + LR+ LG    K GCD G+CGACTVL++G+P  AC T AH V
Sbjct: 14  LNGREAAPMLFPGQRLSEVLREGLGQRDVKIGCDAGDCGACTVLIEGEPVCACLTPAHQV 73

Query: 69  AGHSIETIEGL-SHEGNLSRLQRAFHEHLGSQCGFCTPGMIMAAEALLRRNPQPSRDEIR 127
           AG  +ET++GL +++   ++L ++F +H  +QCG CTPGM+++A ALLR  P+P+  +++
Sbjct: 74  AGREVETVQGLHANDPVAAKLAQSFLDHGAAQCGICTPGMMVSAVALLRDVPEPTEAQVQ 133

Query: 128 AALAGNLCRCTGYVKIIESVEAA 150
            AL G LCRCTGY KII++V  A
Sbjct: 134 DALGGVLCRCTGYRKIIDAVMGA 156


Lambda     K      H
   0.320    0.135    0.412 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 427
Number of extensions: 28
Number of successful extensions: 2
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 158
Length of database: 911
Length adjustment: 30
Effective length of query: 128
Effective length of database: 881
Effective search space:   112768
Effective search space used:   112768
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 49 (23.5 bits)

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

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About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see:

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory